This is based on a manga series that I haven't read. It first aired in 2002 (though I didn't see it until 2004), but it was preceded by a Ghost in the Shell movie in 1995 (which I didn't see until 2014).
Anyway, the show's set in 2030. Technology has advanced quite a bit. There are cyborgs and people with cyberbrains and stuff like that. (Cyborgs have "ghosts," which I guess means souls.) All this leads to all sorts of high tech crimes, which are dealt with by an agency called Public Security Section 9, which is run by Chief Daisuke Aramaki. The main field operative is a cyborg woman named Major Motoko Kusanagi. Other agents include Batou (another cyborg), Togusa, Ishikawa, Saito, Boma, and Pazu. Section 9 also uses these sort of spider tank things called Tachikoma, which have AIs (but not ghosts), and they're all supposed to have the same personality and memories. However, eventually they start to develop individuality, which is interesting, but it troubles the humans and cyborgs. I won't say too much about that, although I will say the Tachikomas are one of my favorite parts of the series.

As for the title "Stand Alone Complex," well, that's a bit complicated. In part it refers to the fact that some episodes (in the first season) are "stand alone," about sort of isolated cases Section 9 deals with, while the "complex" episodes are part of an ongoing storyline about a mysterious elite hacker known as the Laughing Man. However, "stand alone complex" also refers to a sort of mental or sociological complex that I'm afraid I didn't entirely follow. I dunno, whatever it described in the course of the series, particularly in the second season, didn't seem entirely consistent to me, as if the term may actully have had several slightly different meanings. Or perhaps I'm completely wrong about that. Though one explanation was surely that there could be copycat crimes that... are copying... well, a criminal who never existed. Or something, I dunno. It's weird. And like I said, I still think the term was sometimes used to mean other things. Sort of. Whatever, the series also includes lots of literary and philosophical references, and does a great deal of its own philosophizing about society and technology and psychology and the connections between things, and whatnot. Yes, it was often too complicated for me to follow, but I thought it was very good anyway. Even the stuff I didn't follow, I enjoyed. And hopefully someday I'll watch it all again and try harder to follow everything.

The second season is referred to as 2nd GIG (Manga.com; Wikipedia). Where the first season was divided into "stand alone" and "complex" episodes, 2nd GIG is divided up into "Individual," "Dividual," and "Dual" episodes. Which I'm afraid I didn't manage to follow at all. And the ongoing story-arc for the season was alot more complicated than in the first season. There's a new prime minister named Yoko Kayabuki, who would be a great help to Section 9. And they did their best to help her, especially Aramaki. Unfortunately, her job was complicated because her own government mostly thought of her as little more than a figurehead, and had agendas different from her own. The main problem was all the Asian refugees living in Japan, and debate over what should be done about them, while the refugees themselves were becoming restless and unhappy about their situation. A rebellion could easily develop. And in the early part of the season, there were crimes being committed either by a group calling themselves "the Individual Eleven" (named after some obscure essay that had apparently been written years ago by a philosopher named Patrick Sylvestre); or else stand alone complex copycat crimes created in the name of the Individual Eleven. Of course I had a great deal of trouble following all that was going on, and then... the group killed themselves. I think they all had some kind of virus in their cyberbrains that caused them to commit the crimes in the first place, as well as eventually committing group suicide.

Only one of them survived, a man called Hideo Kuze, who became a leader to the refugees. He had a prosthetic body, like Kusanagi and Batou, although his lips don't move when he speaks. He also had found a way to allow millions of refugees to link to his cyberbrain at once, while still keeping out unwanted people who might try to hack in. Meanwhile, the head of the Cabinet Intelligence Agency, Kazundo Gouda (who had risen to power after his face had been disfigured at some point), had his own agenda involving the refugees, and he also had an ally in Chief Cabinet Secretary Takakura, who mainly seemed to want to get rid of Kayabuki and also produce a state of affairs in Japan that would be conducive to a military build-up. Plus they seem to have had some kind of alliance with the American Empire. Of course, there were a great many different agencies involved in the plot, each with their own acronym, and I just couldn't follow it all. (I'm saying that a lot, aren't I?) But despite all the complicated machinations, there was still time to learn a bit about various members of Section 9, on a personal level, and of course further development of the Tachikomas, which was always fun. They may even have developed their own ghosts....

Anyway, in the end the plot basically boiled down to Kuze trying to advance his plans for a kind of revolution that was ultimately more like evolution... and Gouda counting on Kuze's actions to unwittingly advance his own plans to destabilize Japan for his own purposes. And Section 9 was stuck in the middle, along with Kayabuki. Oh yeah, I should also mention there were a few new recruits for Section 9 this season: Azuma, Yano, and a prototype bioandroid called Proto. And that's about all I can think to say about 2nd GIG, for now.

Anyway, despite the fact that I only partially managed to follow everything that was going on, let alone all the philosophizing and whatnot, it's a very, very interesting series. I quite like everything about it: the stories, the characters, the animation, the action, the music (by the brilliant composer Yoko Kanno, who of course does the music in so many great animes), and just generally the deepness and complexity of it all.

In 2006 there was an OVA movie called "Solid State Society," which I haven't seen yet, but I'd certainly like to.